Genome wide association studies reveal an evolutionary conserved locus associated with polyembryony in Mangifera indica L

Authors: Ali, Gul; LI, JIN - Oak Ridge Institute For Science And Education (ORISE); SHAMSELDEEN, ELTAHER - Oak Ridge Institute For Science And Education (ORISE); Freeman, Barbara

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2025
Publication Date: 1/29/2025
Citation: Ali, G.S., Li, J., Shamseldeen, E., Freeman, B.L. 2025. Genome wide association studies reveal an evolutionary conserved locus associated with polyembryony in Mangifera indica L. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2025.1508027.
DOI: https://doi.org/10.3389/fpls.2025.1508027

Interpretive Summary: The USDA-ARS National Clonal Germplasm Repository in Miami, Florida maintains a large collection of mangoes (Mangifera spp.), which date back to early 20th century. These resources provide important genetic material for basic and applied research. The entire collection is evaluated for various horticultural and fruit quality traits, which are provided to stakeholders through GRIN-global.org. Leveraging latest developments in DNA sequencing technologies and high-resolution genomics, using Genome-Wide Association Studies (GWAS), molecular markers were identified for the polyembryony trait in mango. Polyembryony is important for clonally propagating elite cultivars through seeds, particularly in fruit trees, which have distinct and highly heterozygous fixed genotypes. Understanding the genetic mechanism of polyembryony will result in accelerating breeding new mango cultivars. Implementation of marker-assisted selection for polyembryony at the early seedling stage will substantially reduce operational costs associated with maintaining breeding populations of mango trees over multiple years and locations. Other applications of findings in this report include expanding polyembryony to other fruit crops in the anacardiaceous family and beyond.

Technical Abstract: Apomixis – the production of asexual seeds from unreduced maternal cells in the ovule without meiosis – is an important horticultural trait, which allows clonal propagation of hybrids. Many polyembryonic mango cultivars display apomictic polyembryony, in which one embryo develops from zygotic tissues and the rest from nucellar tissues, which give rise to seedlings that are genetically identical to the mother tree. Polyembryony is a natural vegetative reproduction method, which fixes desirable genotypes and is useful for clonally propagating heterozygous fruit trees through seeds. In Mangifera indica L. commercially important rootstocks are usually raised from apomictic seeds, which are then grafted with the scions of desired cultivars. Understanding the genetics and finding molecular markers for polyembryony would facilitate introgression of this trait in commercially important mango cultivars. In this report, using genome-wide association studies conducted with high-density single nucleotide polymorphism (SNP) markers on a diversity panel consisting of 42 polyembryonic and 42 monoembryonic M. indica cultivars, the apomictic polyembryony locus was delineated to a single 360-kb locus on linkage group 17 of the M. indica Cv. 'Alphonso' reference genome. This locus contains the MiRWP/MiRKD4 gene, which codes for an RWP–RK domain–containing protein, and which has previously been implicated in apomixis in citrus. Comparative genomic analyses revealed synteny between the citrus and the mango polyembryony loci suggesting a common evolutionary mechanism for this trait. A total of 29 high quality SNP markers in this locus were found to be significantly associated with polyembryony in M. indica. Any of these SNP markers, especially those flanking the MiRWP/MiRKD4 gene (LOC123199943) provide a valuable tool for mango breeders to select polyembryonic progenies at the seedling stages in mango breeding programs. Given the conservation of polyembryonic locus between citrus and mangoes, polyembryony could be potentially introduced into related tree crops using genome editing.